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Top 10: Questions Not-for-Profits should Ask Their Accountants Regarding Form 990

This is another posting in the MinistryCPA Top 10 series:

Filing your not-for-profit (NFP) organization government reports can be a daunting task, even more stressful than Form 1040. We have compiled a list of some of the top questions that we have received when dealing with Form 990. We recommend that NFPs consider asking their accountants these questions. This list is by no means comprehensive, but it does cover some of the areas for which we receive the most questions.  

1. Does the organization need to file a Form 990? 

The IRS has established a list of requirements to help tax-exempt organizations determine whether they need to file Form 990 and which one to file. Most not-for-profit organizations need to file Form 990, but if the organization is small enough it may only need to file an e-postcard (990-N). Churches are automatically recognized as a tax-exempt organization and generally exempt from filing Form 990. The IRS has published articles that give comprehensive lists of organizations which need to file a 990.

2. Which 990 should the organization file?

There are four different 990 types. The following list breaks down each 990 and when an organization should use each one.

  • 990-N
    • Gross receipts <$50,000
  • 990-EZ
    • Gross receipts <$200,000 and Total assets <$500,000
  • 990
    • Gross receipts >$200,000 or Total assets >$500,000
  • 990-PF
    • Private foundation, regardless of financial status

3. What is the relationship between Form 1023 and Form 990?

Form 1023 is the form that is required before an organization is recognized by the IRS as tax exempt. Churches do not need to file Form 1023 since they are automatically recognized as non-profit organizations. However, there is one advantage to filing Form 1023 even though a church is automatically recognized as tax exempt. Organizations, including churches, that file Form 1023 are listed on the IRS's non-profit lookup site. Some grant issuing organizations and businesses may require that a non-profit be on that list before disbursing grants or making charitable contributions. As with the 990s, there is also a 1023-EZ that is available for organizations that meet certain size requirements.

4. What are the consequences if the 990 is filed late?

The consequences for filing late depend on the size of the organization. If an organization that has less than $1,000,000 in gross receipts files late, the IRS assesses a penalty of $20 per day, not to exceed the lessor of $10,000 or 5% of the organization’s gross receipts. For an organization that has gross receipts greater than $1,000,000 the penalty is increased to $100 per day with a maximum penalty of $50,000.

5. What are the consequences if the nonprofit's tax-exempt status is revoked?

If a tax-exempt organization's status is revoked, there are a few consequences. The first is that the organization must start paying federal income taxes, typically on Form 1120. The second is that any state tax exemptions no longer apply. Third, the real estate tax exemption that a not-for-profit organization enjoys is revoked. Fourth, private foundations will likely discontinue providing grants to the organization since it is no longer a tax-exempt organization. Finally, donors will no longer be able to deduct charitable contributions to the organization. In order to reinstate an organization's non-profit status, the organization must re-apply and receive a letter from the IRS that confirms its tax-exempt status.

6. What accounting records are needed to support the 990?

While nonprofit organizations may operate differently than other for-profit organizations, they still must maintain many of the same documents for financial record keeping purposes. The organization should have documentation that helps it to prove its income and expenses. It should also keep specific record of donors who gave more than $5,000 in a calendar year; this includes information such as their name, address, and how much they donated. This information also helps the organization to perform a public support test to show that it receives its support from the public and not just a small number of donors.

7. What is unrelated business income?

Unrelated business income is income that comes from operations that are outside the scope of the normal activities of the nonprofit organization. Activities that fit this category include operations that are commercial in nature and are regularly carried out by the organization. The NFP can have unrelated business income of up to $1,000 dollars without paying tax, but once that threshold is crossed taxes must be paid. The instructions to Form 990-T answer many of the questions not-for-profit leaders pose related to unrelated business income tax.

8. What does the organization need to track for fundraising events?

There are no set guidelines for fundraising events, which can make it difficult to know what to track. However, there are good practices that should be implemented by nonprofit organizations to help analyze how successful their fundraiser was. NFPs should be tracking each transaction that is made at a fundraiser, as well as all expenses that went into operating the event. These types of records will help the organization analyze how productive the fundraiser was. If the organization receives more than $15,000 in gross income from fundraising, then the organization must also file Schedule G along with its Form 990.

9. What is the difference between "public charity" and "private foundation"?

Public charities are the most common type of not-for-profit organizations. These organizations are funded by a large number of people from the general public. Their purpose is to serve society in some way. Private foundations are also charities, but these organizations are normally funded by a single individual or a very small number of donors. Generally, private foundations must disburse their funds as grants or gifts to other nonprofit organizations. This money often comes from an endowment whose earnings have been designated to be disbursed for exempt purposes.

10. What state tax expectations are there?

Some states require that non-profit organizations file a report similar to Form 990. The state may also require the organization to register the non-profit in the state, or file corporate financial reports.  Every state is different and has different regulations; be sure that the organization understands what its filing requirements are for its state.

While this list represents the top 10 questions we receive about the 990, we recognize that there are certainly more to consider. Please leave your thoughts and suggestions in the comments below, including topics that you would like us to cover. Contact us if we can help you address any of the 990 questions discussed above.

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